How to use - PPIR

Go to content

Main menu:

How to added ptmPPIR in R

1. When in R click on "Packages" menu --> "Install package(s) from local zip files..."

2. Browse for "PtmPPIR_0.5-1.zip" or "PtmPPIR_0.5-1.tar.gz" according to your OS

3. Wait untill PtmPPIR package is installed. If success, you should see message like following figure.

How to use ptmPPIR package

1. When in R type:

library(PtmPPIR)

2. R will then load PtmPPIR into its environment. You also see message "Loading required package: kernlab". This is because PtmPPIR require kernlab package for generating the models.

3. Basically, if you have sequence(s) in mind you can use a command as following:

- If only 1 sequence (must be 15 amino acids long, modifided site at the 8th position)
type:
predPPIR("CPKDEDYKQRTQKKA", ModType="acetylation")
Please note that modtype here can be "acetylation", "ubiquitylation", and "phosphorylation"(case sensitive when typing)

and you will see the result like:
AAseq Res
[1,] "CPKDEDYKQRTQKKA" "Out PPIRs"

This indicates that the modified K (acetylated) is predicted as outside PPIRs by our model.

- If more than 1 sequence (also, must be 15 amino acids long, modifided site at the 8th position)

type:

predPPIR(c("CPKDEDYKQRTQKKA","ESKVFYLKMKGDYYR","RFGISREKQDTFALA","AKNSPLNKAEVHESY"),ModType="acetylation")

and you will see the result like:

AAseq Res

[1,] "CPKDEDYKQRTQKKA" "Out PPIRs"

[2,] "ESKVFYLKMKGDYYR" "In PPIRs"

[3,] "RFGISREKQDTFALA" "Out PPIRs"

[4,] "AKNSPLNKAEVHESY" "Out PPIRs"

This indicates that the modified K at 8th position of "ESKVFYLKMKGDYYR" is predicted as inside PPIRs by our model.

** It is more convenient if you provide the list of your sequences in the text file (one line per sequence)**

Then you can type:

myList = readLines("yourFile.txt")

then

predPPIR(myList, ModType="acetylation")

Free Visits Counter